One of the common misconception about video formats is the confusion between container and media.
The subject is complex, and people willing to learn more can start digging here:
To make things simple:
Audio and video can be coded in hundreds of different algorithms (codec and settings), whereas they are stored in fewer file formats (containers).
A few containers: AIFF, WAV, 3GP, ASF, AVI, Matroska, MPEG, MP4, MOV, Ogg, RealMedia, MXF, VOB, ...
How do containers affect repairability?
Most of the time, Movie Repair has to deal with a broken, incomplete, or missing container: We try to recreate a container for media from scratch.
(Only in rare cases we can take advantage of the original container. This is then a Container structure correction.)
Therefore, the original container is not really important to this regard.
The media format (codec and settings) is far more important to set expectations of a repair.
Repair Service targets original content. In other words, video that has enough value to have a repair fee paid for.
Matroska, OGG, WMV, ASF, FLV and AVI content is usually not original: you can get it again from several sources like Internet, friends, YouTube... Repairing those video files is possible, but very little development has been done in this direction.
Specifics of repairing QuickTime .mov containers
Unless the sample tables inside the moov atom are intact, the repair is not easy.
Media data, from one or several tracks, is laid out continuously, without any header or pattern that would help determine where a frame starts and ends.
Movies with RTP packets (for streaming, webcasting applications) are easier to repair because the packets contain redundant information about audio and video frames nearby.
Specifics of repairing mp4, m4v, MPEG-4 and 3GP containers
Exactly same as QuickTime container, see above.
Specifics of repairing AVI containers
Frames inside an AVI file have a small header, typically '00dc' and '01wc' for audio and video, with the frame length encoded on 32 bits just after. This makes reindexing of AVI files almost trivial if you have basic programming skills.
Specifics of repairing MXF containers
See dedicated page: Corrupt MXF files
Specifics of repairing MPEG containers
Transport streams should never need a repair, by definition. For Program streams, see dedicated MPEG article.